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Protein

SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1

Gene

SMARCB1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Core component of the BAF (hSWI/SNF) complex. This ATP-dependent chromatin-remodeling complex plays important roles in cell proliferation and differentiation, in cellular antiviral activities and inhibition of tumor formation. The BAF complex is able to create a stable, altered form of chromatin that constrains fewer negative supercoils than normal. This change in supercoiling would be due to the conversion of up to one-half of the nucleosomes on polynucleosomal arrays into asymmetric structures, termed altosomes, each composed of 2 histones octamers. Stimulates in vitro the remodeling activity of SMARCA4/BRG1/BAF190A. Involved in activation of CSF1 promoter. Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a postmitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to postmitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth (By similarity). Plays a key role in cell-cycle control and causes cell cycle arrest in G0/G1.By similarity6 Publications

GO - Molecular functioni

  • DNA binding Source: UniProtKB
  • p53 binding Source: BHF-UCL
  • RNA polymerase I CORE element sequence-specific DNA binding Source: UniProtKB
  • Tat protein binding Source: BHF-UCL
  • transcription coactivator activity Source: BHF-UCL

GO - Biological processi

  • ATP-dependent chromatin remodeling Source: UniProtKB
  • cell cycle Source: UniProtKB-KW
  • cell differentiation Source: GO_Central
  • chromatin remodeling Source: BHF-UCL
  • DNA integration Source: ProtInc
  • DNA repair Source: GO_Central
  • negative regulation of cell proliferation Source: GO_Central
  • negative regulation of histone H3-K9 dimethylation Source: UniProtKB
  • negative regulation of histone H3-K9 trimethylation Source: UniProtKB
  • nervous system development Source: UniProtKB-KW
  • nucleosome disassembly Source: BHF-UCL
  • positive regulation by host of viral transcription Source: BHF-UCL
  • positive regulation of DNA binding transcription factor activity Source: BHF-UCL
  • positive regulation of glucose mediated signaling pathway Source: UniProtKB
  • positive regulation of histone H3-K9 acetylation Source: UniProtKB
  • positive regulation of histone H4 acetylation Source: UniProtKB
  • positive regulation of transcription by RNA polymerase II Source: BHF-UCL
  • positive regulation of transcription of nucleolar large rRNA by RNA polymerase I Source: UniProtKB
  • regulation of transcription by RNA polymerase II Source: ProtInc
  • single stranded viral RNA replication via double stranded DNA intermediate Source: MGI

Keywordsi

Molecular functionActivator, Chromatin regulator, DNA-binding
Biological processCell cycle, Host-virus interaction, Neurogenesis, Transcription, Transcription regulation

Enzyme and pathway databases

ReactomeiR-HSA-3214858 RMTs methylate histone arginines
R-HSA-8939243 RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known
SIGNORiQ12824

Names & Taxonomyi

Protein namesi
Recommended name:
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1
Alternative name(s):
BRG1-associated factor 47
Short name:
BAF47
Integrase interactor 1 protein
SNF5 homolog
Short name:
hSNF5
Gene namesi
Name:SMARCB1
Synonyms:BAF47, INI1, SNF5L1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 22

Organism-specific databases

EuPathDBiHostDB:ENSG00000099956.18
HGNCiHGNC:11103 SMARCB1
MIMi601607 gene
neXtProtiNX_Q12824

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Involvement in diseasei

Rhabdoid tumor predisposition syndrome 1 (RTPS1)2 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA familial cancer syndrome predisposing to renal or extrarenal malignant rhabdoid tumors and to a variety of tumors of the central nervous system, including choroid plexus carcinoma, medulloblastoma, and central primitive neuroectodermal tumors. Rhabdoid tumors are the most aggressive and lethal malignancies occurring in early childhood.
See also OMIM:609322
Schwannomatosis 1 (SWNTS1)2 Publications
Disease susceptibility is associated with variations affecting the gene represented in this entry.
Disease descriptionA cancer syndrome in which patients develop multiple non-vestibular schwannomas, benign neoplasms that arise from Schwann cells of the cranial, peripheral, and autonomic nerves.
See also OMIM:162091
Coffin-Siris syndrome 3 (CSS3)3 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA form of Coffin-Siris syndrome, a congenital multiple malformation syndrome with broad phenotypic and genetic variability. Cardinal features are intellectual disability, coarse facial features, hypertrichosis, and hypoplastic or absent fifth digit nails or phalanges. Additional features include malformations of the cardiac, gastrointestinal, genitourinary, and/or central nervous systems. Sucking/feeding difficulties, poor growth, ophthalmologic abnormalities, hearing impairment, and spinal anomalies are common findings. Both autosomal dominant and autosomal recessive inheritance patterns have been reported.
See also OMIM:614608
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_08026337R → H in CSS3; patient with original diagnosis of Kleefstra syndrome; unknown pathological significance. 1 PublicationCorresponds to variant dbSNP:rs398122368EnsemblClinVar.1
Natural variantiVAR_068178364Missing in CSS3. 1 Publication1
Natural variantiVAR_076934366R → C in CSS3. 1 PublicationCorresponds to variant dbSNP:rs886039520EnsemblClinVar.1
Natural variantiVAR_076935374R → Q in CSS3. 1 PublicationCorresponds to variant dbSNP:rs1057517825Ensembl.1
Natural variantiVAR_068179377R → H in CSS3. 1 PublicationCorresponds to variant dbSNP:rs387906812EnsemblClinVar.1

Keywords - Diseasei

Disease mutation, Hypotrichosis, Mental retardation, Tumor suppressor

Organism-specific databases

DisGeNETi6598
GeneReviewsiSMARCB1
MalaCardsiSMARCB1
MIMi162091 phenotype
609322 phenotype
614608 phenotype
OpenTargetsiENSG00000099956
Orphaneti99966 Atypical teratoid rhabdoid tumor
1465 Coffin-Siris syndrome
263662 Familial multiple meningioma
231108 Familial rhabdoid tumor
93921 Neurofibromatosis type 3
PharmGKBiPA35953

Polymorphism and mutation databases

BioMutaiSMARCB1
DMDMi51338799

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002059481 – 385SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1Add BLAST385

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki106Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki108Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki124Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei129PhosphoserineCombined sources1
Cross-linki161Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources

Keywords - PTMi

Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ12824
MaxQBiQ12824
PaxDbiQ12824
PeptideAtlasiQ12824
PRIDEiQ12824
ProteomicsDBi58970
58971 [Q12824-2]

PTM databases

iPTMnetiQ12824
PhosphoSitePlusiQ12824

Expressioni

Gene expression databases

BgeeiENSG00000099956
CleanExiHS_SMARCB1
ExpressionAtlasiQ12824 baseline and differential
GenevisibleiQ12824 HS

Organism-specific databases

HPAiCAB009196
HPA018248
HPA019127

Interactioni

Subunit structurei

Component of the multiprotein chromatin-remodeling complexes SWI/SNF: SWI/SNF-A (BAF), SWI/SNF-B (PBAF) and related complexes. The canonical complex contains a catalytic subunit (either SMARCA4/BRG1/BAF190A or SMARCA2/BRM/BAF190B) and at least SMARCE1, ACTL6A/BAF53, SMARCC1/BAF155, SMARCC2/BAF170, and SMARCB1/SNF5/BAF47. Other subunits specific to each of the complexes may also be present permitting several possible combinations developmentally and tissue specific (Probable). Component of the BAF complex, which includes at least actin (ACTB), ARID1A/BAF250A, ARID1B/BAF250B, SMARCA2/BRM, SMARCA4/BRG1/BAF190A, ACTL6A/BAF53, ACTL6B/BAF53B, SMARCE1/BAF57 SMARCC1/BAF155, SMARCC2/BAF170, SMARCB1/SNF5/INI1, and one or more SMARCD1/BAF60A, SMARCD2/BAF60B, or SMARCD3/BAF60C. In muscle cells, the BAF complex also contains DPF3 (PubMed:8895581, PubMed:18765789). Component of neural progenitors-specific chromatin remodeling complex (npBAF complex) composed of at least, ARID1A/BAF250A or ARID1B/BAF250B, SMARCD1/BAF60A, SMARCD3/BAF60C, SMARCA2/BRM/BAF190B, SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, SMARCC1/BAF155, SMARCE1/BAF57, SMARCC2/BAF170, PHF10/BAF45A, ACTL6A/BAF53A and actin. Component of neuron-specific chromatin remodeling complex (nBAF complex) composed of at least, ARID1A/BAF250A or ARID1B/BAF250B, SMARCD1/BAF60A, SMARCD3/BAF60C, SMARCA2/BRM/BAF190B, SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, SMARCC1/BAF155, SMARCE1/BAF57, SMARCC2/BAF170, DPF1/BAF45B, DPF3/BAF45C, ACTL6B/BAF53B and actin (By similarity). Component of the SWI/SNF-B (PBAF) chromatin remodeling complex, at least composed of SMARCA4/BRG1, SMARCB1/BAF47/SNF5, ACTL6A/BAF53A or ACTL6B/BAF53B, SMARCE1/BAF57, SMARCD1/BAF60A, SMARCD2/BAF60B, perhaps SMARCD3/BAF60C, SMARCC1/BAF155, SMARCC2/BAF170, PBRM1/BAF180, ARID2/BAF200 and actin (PubMed:26601204). Binds to double-stranded DNA. Interacts with CEBPB (when not methylated) (PubMed:20111005). Interacts with PIH1D1 (PubMed:22368283). Interacts with MYK and MAEL (PubMed:10319872). Interacts with PPP1R15A (PubMed:10490642, PubMed:12016208).2 PublicationsBy similarity7 Publications
(Microbial infection) Binds tightly to the human immunodeficiency virus-type 1 (HIV-1) integrase in vitro and stimulates its DNA-joining activity. Interacts with human papillomavirus 18 E1 protein to stimulate its viral replication (PubMed:10365963). Interacts with Epstein-Barr virus protein EBNA-2 (PubMed:8709224).2 Publications

Binary interactionsi

Show more details

GO - Molecular functioni

  • p53 binding Source: BHF-UCL
  • Tat protein binding Source: BHF-UCL

Protein-protein interaction databases

BioGridi112482, 186 interactors
CORUMiQ12824
DIPiDIP-27550N
IntActiQ12824, 64 interactors
MINTiQ12824
STRINGi9606.ENSP00000263121

Structurei

Secondary structure

1385
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi16 – 18Combined sources3
Beta strandi25 – 28Combined sources4
Helixi29 – 36Combined sources8
Helixi42 – 46Combined sources5
Beta strandi52 – 54Combined sources3
Helixi57 – 66Combined sources10
Beta strandi72 – 74Combined sources3
Beta strandi89 – 92Combined sources4
Helixi93 – 101Combined sources9
Helixi105 – 108Combined sources4
Beta strandi186 – 195Combined sources10
Beta strandi198 – 207Combined sources10
Beta strandi211 – 213Combined sources3
Helixi215 – 226Combined sources12
Helixi230 – 247Combined sources18
Beta strandi259 – 261Combined sources3

3D structure databases

ProteinModelPortaliQ12824
SMRiQ12824
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati186 – 2451Add BLAST60
Repeati259 – 3192Add BLAST61

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 113DNA-binding1 PublicationAdd BLAST113
Regioni183 – 243HIV-1 integrase-bindingAdd BLAST61
Regioni186 – 3192 X approximate tandem repeatsAdd BLAST134
Regioni186 – 245MYC-binding1 PublicationAdd BLAST60
Regioni304 – 318Interaction with PPP1R15A1 PublicationAdd BLAST15

Domaini

The N-terminal DNA-binding region is structurally similar to winged helix domains.1 Publication

Sequence similaritiesi

Belongs to the SNF5 family.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG1649 Eukaryota
ENOG410XSZD LUCA
GeneTreeiENSGT00440000038585
HOGENOMiHOG000015760
HOVERGENiHBG011709
InParanoidiQ12824
KOiK11648
PhylomeDBiQ12824
TreeFamiTF105993

Family and domain databases

InterProiView protein in InterPro
IPR017393 Sfh1/SNF5
IPR006939 SNF5
PANTHERiPTHR10019 PTHR10019, 1 hit
PfamiView protein in Pfam
PF04855 SNF5, 2 hits
PIRSFiPIRSF038126 SWI_SNF, 1 hit

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform A (identifier: Q12824-1) [UniParc]FASTAAdd to basket
Also known as: INI1A

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MMMMALSKTF GQKPVKFQLE DDGEFYMIGS EVGNYLRMFR GSLYKRYPSL
60 70 80 90 100
WRRLATVEER KKIVASSHGK KTKPNTKDHG YTTLATSVTL LKASEVEEIL
110 120 130 140 150
DGNDEKYKAV SISTEPPTYL REQKAKRNSQ WVPTLPNSSH HLDAVPCSTT
160 170 180 190 200
INRNRMGRDK KRTFPLCFDD HDPAVIHENA SQPEVLVPIR LDMEIDGQKL
210 220 230 240 250
RDAFTWNMNE KLMTPEMFSE ILCDDLDLNP LTFVPAIASA IRQQIESYPT
260 270 280 290 300
DSILEDQSDQ RVIIKLNIHV GNISLVDQFE WDMSEKENSP EKFALKLCSE
310 320 330 340 350
LGLGGEFVTT IAYSIRGQLS WHQKTYAFSE NPLPTVEIAI RNTGDADQWC
360 370 380
PLLETLTDAE MEKKIRDQDR NTRRMRRLAN TAPAW
Length:385
Mass (Da):44,141
Last modified:August 16, 2004 - v2
Checksum:iB7BCA26875BD943D
GO
Isoform B (identifier: Q12824-2) [UniParc]FASTAAdd to basket
Also known as: INI1B

The sequence of this isoform differs from the canonical sequence as follows:
     69-77: Missing.

Show »
Length:376
Mass (Da):43,158
Checksum:i6C7233EAFBC389A9
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti136P → S (PubMed:7801128).Curated1
Sequence conflicti136P → S in CAA76639 (PubMed:9671307).Curated1
Sequence conflicti378L → E in CAA76639 (PubMed:9671307).Curated1
Sequence conflicti382A → G (PubMed:7801128).Curated1
Sequence conflicti382A → G in CAA76639 (PubMed:9671307).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_08026337R → H in CSS3; patient with original diagnosis of Kleefstra syndrome; unknown pathological significance. 1 PublicationCorresponds to variant dbSNP:rs398122368EnsemblClinVar.1
Natural variantiVAR_068178364Missing in CSS3. 1 Publication1
Natural variantiVAR_076934366R → C in CSS3. 1 PublicationCorresponds to variant dbSNP:rs886039520EnsemblClinVar.1
Natural variantiVAR_076935374R → Q in CSS3. 1 PublicationCorresponds to variant dbSNP:rs1057517825Ensembl.1
Natural variantiVAR_068179377R → H in CSS3. 1 PublicationCorresponds to variant dbSNP:rs387906812EnsemblClinVar.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_00439969 – 77Missing in isoform B. 4 Publications9

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U04847 mRNA Translation: AAA81905.1
Y17118
, Y17119, Y17120, Y17121, Y17122, Y17123, Y17124, Y17125, Y17126 Genomic DNA Translation: CAA76639.1 Sequence problems.
AJ011738 mRNA Translation: CAA09759.1
AJ011737 mRNA Translation: CAA09758.1
AB017523 mRNA Translation: BAC77068.1
CR456581 mRNA Translation: CAG30467.1
AK021419 mRNA Translation: BAG51033.1
DQ230988 Genomic DNA Translation: ABB02184.1
CH471095 Genomic DNA Translation: EAW59606.1
BC117114 mRNA Translation: AAI17115.1
BC143667 mRNA Translation: AAI43668.1
CCDSiCCDS13817.1 [Q12824-1]
CCDS46671.1 [Q12824-2]
PIRiS54705
RefSeqiNP_001007469.1, NM_001007468.2 [Q12824-2]
NP_003064.2, NM_003073.4 [Q12824-1]
UniGeneiHs.534350

Genome annotation databases

EnsembliENST00000407422; ENSP00000383984; ENSG00000099956 [Q12824-2]
ENST00000618915; ENSP00000479330; ENSG00000275837 [Q12824-1]
ENST00000631333; ENSP00000486870; ENSG00000275837 [Q12824-2]
ENST00000644036; ENSP00000494049; ENSG00000099956 [Q12824-1]
GeneIDi6598
KEGGihsa:6598
UCSCiuc002zyb.4 human [Q12824-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiSNF5_HUMAN
AccessioniPrimary (citable) accession number: Q12824
Secondary accession number(s): O75784
, O95474, Q17S11, Q38GA1, Q76N08, Q9UBH2
Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: August 16, 2004
Last modified: July 18, 2018
This is version 189 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 22
    Human chromosome 22: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

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